def parse_graph(self, graph=None, context=None):
"""Iterate over RDF model yielding CDAO.Tree instances."""
if graph is None:
graph = self.graph
# look up branch lengths/TUs for all nodes
self.get_node_info(graph, context=context)
for root_node in self.tree_roots:
clade = self.parse_children(root_node)
yield CDAO.Tree(root=clade, rooted=self.rooted)
def new_clade(self, node):
'''Returns a CDAO.Clade object for a given named node.'''
result = self.node_info[node]
kwargs = {}
if 'branch_length' in result: kwargs['branch_length'] = result['branch_length']
if 'label' in result: kwargs['name'] = result['label'].replace('_', ' ')
if 'confidence' in result: kwargs['confidence'] = result['confidence']
clade = CDAO.Clade(**kwargs)
return clade
def parse_graph(self, graph=None, context=None):
'''Generator that yields CDAO.Tree instances from an RDF model.'''
if graph is None:
graph = self.graph
# look up branch lengths/TUs for all nodes
self.get_node_info(graph, context=context)
for root_node in self.tree_roots:
clade = self.parse_children(root_node)
yield CDAO.Tree(root=clade, rooted=self.rooted)
def new_clade(self, node):
"""Return a CDAO.Clade object for a given named node."""
result = self.node_info[node]
kwargs = {}
if "branch_length" in result:
kwargs["branch_length"] = result["branch_length"]
if "label" in result:
kwargs["name"] = result["label"].replace("_", " ")
if "confidence" in result:
kwargs["confidence"] = result["confidence"]
clade = CDAO.Clade(**kwargs)
return clade
def parse_model(self, model=None, context=None):
'''Generator that yields CDAO.Tree instances from an RDF model.'''
if model is None:
model = self.model
if not context is None: context = RDF.Node(RDF.Uri(context))
# look up branch lengths/TUs for all nodes
self.get_node_info(model, context=context)
for root_node in self.tree_roots:
clade = self.parse_children(root_node)
yield CDAO.Tree(root=clade, rooted=self.rooted)
